2LGM

Structure of DNA Containing an Aristolactam II-dA Lesion


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 26 
  • Conformers Submitted: 26 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and stability of DNA containing an aristolactam II-dA lesion: implications for the NER recognition of bulky adducts.

Lukin, M.Zaliznyak, T.Johnson, F.de Los Santos, C.

(2012) Nucleic Acids Res. 40: 2759-2770

  • DOI: 10.1093/nar/gkr1094

  • PubMed Abstract: 
  • Aristolochic acids I and II are prevalent plant toxicants found in the Aristolochiaceae plant family. Metabolic activation of the aristolochic acids leads to the formation of a cyclic N-hydroxylactam product that can react with the peripheral amino g ...

    Aristolochic acids I and II are prevalent plant toxicants found in the Aristolochiaceae plant family. Metabolic activation of the aristolochic acids leads to the formation of a cyclic N-hydroxylactam product that can react with the peripheral amino group of purine bases generating bulky DNA adducts. These lesions are mutagenic and established human carcinogens. Interestingly, although AL-dG adducts progressively disappear from the DNA of laboratory animals, AL-dA lesions has lasting persistence in the genome. We describe here NMR structural studies of an undecameric duplex damaged at its center by the presence of an ALII-dA adduct. Our data establish a locally perturbed double helical structure that accommodates the bulky adduct by displacing the counter residue into the major groove and stacking the ALII moiety between flanking bases. The presence of the ALII-dA perturbs the conformation of the 5'-side flanking base pair, but all other pairs of the duplex adopt standard conformations. Thermodynamic studies reveal that the lesion slightly decreases the energy of duplex formation in a sequence-dependent manner. We discuss our results in terms of its implications for the repair of ALII-dA adducts in mammalian cells.


    Organizational Affiliation

    Department of Pharmacological Sciences, School of Medicine, Stony Brook University, Stony Brook, NY 11794-8651, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*AP*TP*GP*C)-3')111N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*TP*GP*TP*GP*TP*AP*CP*G)-3')211N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A4A
Query on A4A

Download SDF File 
Download CCD File 
1
[1,3]benzodioxolo[6,5,4-cd]benzo[f]indol-5(6H)-one
Aristolactam II
C16 H9 N O3
KPVDACWQNCRKTG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 26 
  • Conformers Submitted: 26 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2012-04-11
    Type: Database references